rs6397899 SNP Detail

Summary

• ID
  rs6397899
• Variation Type
  SNP
• Alleles
  C/T

• Created in dbSNP Build
  116
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser | Alliance Variant
  

Genome Location and Flanking Sequence

• Location
  Chr3:9068795 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              TTATTTACAT TTTCAAAAAC
  TCATTATTGA TACTCATACC AGGTGCAAAC ACCGGAAGCA AATAAGCAGA AAATAAGGAT
  TTCTACAGGG GCTTGCATCA GGAATGATCC CTAAAACCAC TTCCAAAATA CTTAGTATTT
  TCCTTAGCAT TCTATACCCT TTCAAGCCTG CCACCCATAC CAGTTTCATA GCAGAGCTCT
  Y
  CCACGTAGGC AATATTTCAA TTGAAAACCA TCACCTGCTT CTGGCCACAT CTCCGTAGAT
  TCTATTCCGG GCAATTTCAC TTGACTAGCC ATCTTAGGAA GTAAAAGGAA CAGCTTGGTG
  CCGGAAACCA AAGGTTCCCT GCTGTGTGAT TCACCTGGCT GGAAACTAAG ACCCAGATAG
  TGAAAGCTCC CTTCCCCCAA                                            
  
  Y = C/T
  

  
  Note: Sequence in lower case indicates low-complexity or repetitive sequence

  ---

SNP Assays
and
SNP Consensus

Strain alleles of submitted assays, and consensus values for this SNP

Assay ID	Submitter SNP ID	Submitter Handle	Population	ss orientation	Variation Type	C57BL/6J	CZECHII/EiJ
ss8804086	WI_WGS_3_9031098	WI	MOUSE	f	SNP	T	C
SNP Consensus Information
SNP					Consensus Type	C57BL/6J	CZECHII/EiJ
rs6397899					SNP	T	C

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr3:9068795 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi12969	CpG island 12969			163 bp proximal
Rr374475	regulatory region 374475			within coordinates
Rr573365	regulatory region 573365			389 bp distal
Rr573366	regulatory region 573366			within coordinates
Rr573367	regulatory region 573367			694 bp proximal
Rr573368	regulatory region 573368			1824 bp proximal
Tpd52	tumor protein D52			Intron
				Noncoding-Transcript-Variant
Tssr32570	transcription start site region 32570			96 bp downstream
Tssr32571	transcription start site region 32571			687 bp downstream
Tssr32572	transcription start site region 32572			719 bp downstream
Tssr32573	transcription start site region 32573			737 bp downstream
Tssr32574	transcription start site region 32574			889 bp downstream
Tssr32575	transcription start site region 32575			951 bp downstream
Tssr32576	transcription start site region 32576			1025 bp downstream